We propose an in depth study of the structural mechanics, dynamics and energetics of a family of dihydrofolate reductase (DHFR) systems. The long range goals involve the understanding of such fundamental biological processes as biological recognition, enzyme specificity and regulation and protein architecture. We shall bring an array of theoretical tools to bear on these problems. The first phase of the work involves validation and testing of the theorectical methods. We will carry out extensive molecular dynamics simulations made possible by taking advantage of recent developments in computer technology (300K configurations) of the ternary complexes of DHFR multiplied by NADPH multiplied by Inhibitor complexes in the crystalline state. This will be the first computation of the dynamics, structure and temperature factors of an enzyme complex in the environment in which these properties were measured, making a valid comparison possible. This research program depends critically on the close collaboration with experimentalists; Prof. Joseph Kraut, who is carrying out an extensive investigation of reductase complexes by X-ray and Prof. John Abelson, who is now doing site specific mutagenesis of the DHFR gene in E. Coli. Together with Drs. Kraut and Mathews of UCSD we will use the X-ray structure to test and verify the results of the theorectical treatment, and where necessary to reveal deficiencies which require further understanding and correction. The completion of this stage will lead to an understanding of these systems at the level of the operative interatomic forces, energetics and dynamics determing their properties. At this point we shall once again enter into interactive mode with experiment. Using molecular dynamics, convergent energy minimization and vibrational normal mode analysis, we propose to rationalize the basis for inhibition of these enzymes and the important species dependence of inhibition which is one of the major factors determining the ultimate power of such drugs as the antibiotic trimethorprim. The final stages involve the design and prediction of the affinity of specific inhibitors, again tested experimentally. Finally, we propose to simulate the structural changes accompanying key changes in the amino acid sequence of DHFR, with the ultimate goal of understanding protein architecture and designing specificity or function. Again, these simulations will be checked against the experimental products obtained from the altered gene.